Switch LAPIS for open to v2 by default

- also new 'lintype' option in README.md
cbg-ethz · May 30, 2024 · 84cfa22 · 84cfa22
1 parent 04379d0
commit 84cfa22
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Showing 4 changed files with 15 additions and 7 deletions.
diff --git a/README.md b/README.md
@@ -149,8 +149,12 @@ Usage: cojac cooc-curate [OPTIONS] [VOC]...
 
 Options:
   -u, --url URL               url to use when querying covspectrum (e.g.
-                              https://lapis.cov-spectrum.org/open/v1,
-                              https://lapis.cov-spectrum.org/gisaid/v1, etc.)
+                              https://lapis.cov-spectrum.org/open/v2,
+                              https://lapis.cov-spectrum.org/gisaid/v2, etc.)
+  --lintype FIELD             switch the lineage field queried on covspectrum
+                              (e.g. nextcladePangoLineage: as determined with
+                              nextclade, pangoLineage: as provided by upstream
+                              sequence repository)
   -a, --amplicons YAML        use the YAML file generated by mutbamscan to
                               query amplicons instead of mutations
   -m, --mutations             always do mutations (even if amplicons YAML
@@ -195,8 +199,12 @@ Usage: cojac sig-generate [OPTIONS]
 
 Options:
   -u, --url URL           url to use when querying covspectrum (e.g.
-                          https://lapis.cov-spectrum.org/open/v1,
-                          https://lapis.cov-spectrum.org/gisaid/v1, etc.)
+                          https://lapis.cov-spectrum.org/open/v2,
+                          https://lapis.cov-spectrum.org/gisaid/v2, etc.)
+  --lintype FIELD         switch the lineage field queried on covspectrum
+                          (e.g. nextcladePangoLineage: as determined with
+                          nextclade, pangoLineage: as provided by upstream
+                          sequence repository)
   --var, --variant PANGO  Pangolineage of the root variant to list  [required]
   --extras LAPIS          Additional LAPIS query arguments passed as a YAML
                           flow, e.g.: '{dateFrom: "2022-02-01", variantQuery:

diff --git a/cojac/cooc_curate.py b/cojac/cooc_curate.py
@@ -21,7 +21,7 @@
 #
 
 
-server = "https://lapis.cov-spectrum.org/open/v1"
+server = "https://lapis.cov-spectrum.org/open/v2"
 lintype = "nextcladePangoLineage"
 debug = False
 

diff --git a/cojac/sig_generate.py b/cojac/sig_generate.py
@@ -27,7 +27,7 @@
     required=False,
     default=None,
     type=str,
-    help="url to use when querying covspectrum (e.g. https://lapis.cov-spectrum.org/open/v1, https://lapis.cov-spectrum.org/gisaid/v1, etc.)",
+    help="url to use when querying covspectrum (e.g. https://lapis.cov-spectrum.org/open/v2, https://lapis.cov-spectrum.org/gisaid/v2, etc.)",
 )
 @click.option(
     "--lintype",

diff --git a/tests/test_integration.py b/tests/test_integration.py
@@ -47,7 +47,7 @@ def test_workflow():
             "cojac",
             "sig-generate",
             "--url",
-            "https://lapis.cov-spectrum.org/open/v1",
+            "https://lapis.cov-spectrum.org/open/v2",
             "--variant",
             "BA.1",
         ]